Steps to reproduce:
1. create a new Standalone Module with Action "ShowOpenWindows" implemented like this:
public void actionPerformed(ActionEvent e) {
        Set<TopComponent> opened = WindowManager.getDefault().getRegistry().getOpened();
        for (TopComponent topComponent : opened) {
            System.out.println("opened "+topComponent);
        }
    }
2. Open one or more Editor Windows.
3. Invoke ShowOpenWindowsAction. The Editors will be printed to System.out
4. Invoke "Reset Windows". The Editor Windows will stay open.
5. Invoke ShowOpenWindowsAction again. The Editors will not be printed to System.out.

If you replace the use of Registry with the following code, it will work as expected instead:
Mode editor = WindowManager.getDefault().findMode("editor");
TopComponent[] opened = WindowManager.getDefault().getOpenedTopComponents(editor); 

Background:

"Reset Windows" clears the openSet of the RegistryImpl, but subsequently only updates the Mode Model with the opened Editor TCs, not the Registries openSet. The only code that adds TCs to openSet is in topComponentOpened; it seems this isn't called during reset. 

All Non-Editor-TopComponents are closed during reset and reopened by calling WindowSystem.load(), thereby calling topComponentOpened and reregistering them correctly in Registry. Editors are not closed by ResetWindowsAction, but kept in open state.